tbuckley/cabot-search huggingface dataset:
Are we there yet? Every computational theory needs a few black boxes, including theories about groups
Authors: Andrew W. Delton
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski exemplifies the need for computational theory using group conflict; I complement this with an example of group cooperation. He criticizes past theories for having black boxes; I suggest his theory also has a black box – the concept of costs. He divides what mentally constitutes a group from mere ancillary attributes; I hazard that some of these attributes are essential.
The labelled container: Conceptual development of social group representations
Authors: Rebekah A Gelpi, Suraiya Allidina, Daniel Hoyer, William A Cunningham
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski contends that group representations that rely on a “containment metaphor” fail to adequately capture phenomena of group dynamics such as shifts in allegiances. We argue, in contrast, that social categories allow for computationally efficient, richly structured, and flexible group representations that explain some of the most intriguing aspects of social group behaviour.
Duo Cadherin‐Functionalized Microparticles Synergistically Induce Chondrogenesis and Cartilage Repair of Stem Cell Aggregates (Adv. Healthcare Mater. 13/2022)
Authors: Xueping Wang, Xingquan Xu, Yan Zhang, Xueying An, Xue Zhang, Guoqiang Chen, Qing Jiang, Jun Yang
Journal: Advanced Healthcare Materials (2022)
On vagueness and parochialism in psychological research on groups
Authors: Kyle G. Ratner, David L. Hamilton, Marilynn B. Brewer
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski asserts that social psychological research on groups is too vague, tautological, and dependent on intuitions to be theoretically useful. We disagree. Pietraszewski's contribution is thought-provoking but also incomplete and guilty of many of the faults he attributes to others. Instead of rototilling the existing knowledge landscape, we urge for more integration of new and old ideas.
Thrombocytopenia, anasarca, and severe inflammation
Authors: Amanallah Montazeripouragha, Christine M. Campbell, James Russell, Nadia Medvedev, Daniel R. Owen, Alison Harris, Fergal Donnellan, Iain McCormick, David C. Fajgenbaum, Luke Y. C. Chen
Journal: American Journal of Hematology (2022)

The authors declare no conflict of interest. Data sharing not applicable - no new data generated.
Advantages and limitations of representing groups in terms of recursive utilities
Authors: Setayesh Radkani, Ashley J Thomas, Rebecca Saxe
Journal: Behavioral and Brain Sciences (2022)

Abstract Group representations based on recursive utilities can be used to derive the same predictions as Pietraszewski in conflict situations. Additionally, these representations generalize to non-conflict situations, asymmetric relationships, and represent the stakes in a conflict. However, both proposals fail to represent asymmetries of power and responsibility and to account for generalizations from specific observed individuals to collections of non-observed individuals.
Reply to Yang Zhao, Wenda Wang, and Yushi Zhang’s Letter to the Editor re: Sounak Gupta, Christine M. Lohse, Ross Rowsey, et al. Renal Neoplasia in Polycystic Kidney Disease: An Assessment of Tuberous Sclerosis Complex–associated Renal Neoplasia and PKD1/TSC2 Contiguous Gene Deletion Syndrome. Eur Urol 2022;81:229–33
Authors: Sounak Gupta, Christine M. Lohse, Rafael E. Jimenez, John C. Cheville
Journal: European Urology (2022)
Selexipag for inoperable CTEPH: why meeting a primary endpoint simply isn't enough
Authors: Hossein-Ardeschir Ghofrani
Journal: European Respiratory Journal (2022)

<b>Though this study met its primary endpoint and oral selexipag was approved as a treatment for inoperable CTEPH patients in Japan, the overall results and scope of this study do not justify a valid position for selexipag in the treatment armamentarium.</b>https://bit.ly/3INAYgO
When I use a word . . . . Unnecessary, hateful, sickening words
Authors: Jeffrey K Aronson
Journal: BMJ (2022)

Among many pairs of words that can be confused with one another, odious and otiose are currently of interest. “Odious” means disagreeable, hateful, repugnant, or offensive. “Otiose” simply means unnecessary. In his resignation letter as Boris Johnson9s ethics adviser on 15 June 2022, Lord Geidt described his position as “odious.” One wonders if he also found his boss otiose. This brings to mind the confusion that can occur between “nauseous” and “nauseated”; the latter means feeling sick, the former sickening.
Hepatocellular carcinoma: measures to improve the outlook in sub-Saharan Africa
Authors: C Wendy Spearman, Geoffrey Dusheiko, Eduard Jonas, Abdelmounem Abdo, Mary Afihene, Lina Cunha, Hailemichael Desalegn, Chris Kassianides, Leolin Katsidzira, Anna Kramvis, Philip Lam, Olufunmilayo A Lesi, Eileen A Micah, Emmanuel Musabeyezu, Gibril Ndow, Chidi V Nnabuchi, Ponsiano Ocama, Edith Okeke, John Rwegasha, Abate B Shewaye, Fatuma F Some, Christian Tzeuton, Mark W Sonderup
Journal: The Lancet. Gastroenterology & hepatology (2022)
Allergen protease-activated stress granule assembly and gasdermin D fragmentation control interleukin-33 secretion
Authors: Wen Chen, Shuangfeng Chen, Chenghua Yan, Yaguang Zhang, Ronghua Zhang, Min Chen, Shufen Zhong, Weiguo Fan, Songling Zhu, Danyan Zhang, Xiao Lu, Jia Zhang, Yuying Huang, Lin Zhu, Xuezhen Li, Dawei Lv, Yadong Fu, Houkun Iv, Zhiyang Ling, Liyan Ma, Hai Jiang, Gang Long, Jinfang Zhu, Dong Wu, Bin Wu, Bing Sun
Journal: Nature Immunology (2022)
Deep learning solution for medical image localization and orientation detection
Authors: Yu Zhao, Ke Zeng, Yiyuan Zhao, Parmeet Bhatia, Mahesh Ranganath, Muhammed Labeeb Kozhikkavil, Chen Li, Gerardo Hermosillo
Journal: Medical Image Analysis (2022)

Magnetic Resonance (MR) imaging plays an important role in medical diagnosis and biomedical research. Due to the high in-slice resolution and low through-slice resolution nature of MR imaging, the usefulness of the reconstruction highly depends on the positioning of the slice group. Traditional clinical workflow relies on time-consuming manual adjustment that cannot be easily reproduced. Automation of this task can therefore bring important benefits in terms of accuracy, speed and reproducibility. Current auto-slice-positioning methods rely on automatically detected landmarks to derive the positioning, and previous studies suggest that a large, redundant set of landmarks are required to achieve robust results. However, a costly data curation procedure is needed to generate training labels for those landmarks, and the results can still be highly sensitive to landmark detection errors. More importantly, a set of anatomical landmark locations are not naturally produced during the standard clinical workflow, which makes online learning impossible. To address these limitations, we propose a novel framework for auto-slice-positioning that focuses on localizing the canonical planes within a 3D volume. The proposed framework consists of two major steps. A multi-resolution region proposal network is first used to extract a volume-of-interest, after which a V-net-like segmentation network is applied to segment the orientation planes. Importantly, our algorithm also includes a Performance Measurement Index as an indication of the algorithm's confidence. We evaluate the proposed framework on both knee and shoulder MR scans. Our method outperforms state-of-the-art automatic positioning algorithms in terms of accuracy and robustness.
Race, rituximab, and relapse in TTP
Authors: Shruti Chaturvedi, Ana G. Antun, Andrew M. Farland, Ryan Woods, Ara Metjian, Yara A. Park, Gustaaf de Ridder, Briana Gibson, Raj S. Kasthuri, Darla K. Liles, Frank Akwaa, Todd Clover, Lisa Baumann Kreuziger, J. Evan Sadler, Meera Sridharan, Ronald S. Go, Keith R. McCrae, Harsh Vardhan Upreti, Angela Liu, Ming Y. Lim, Radhika Gangaraju, X. Long Zheng, Jay S. Raval, Camila Masias, Spero R. Cataland, Andrew Johnson, Elizabeth Davis, Michael D. Evans, Marshall A. Mazepa
Journal: Blood (2022)
Serious adverse event rates and reoperation after arthroscopic shoulder surgery: population based cohort study
Authors: Jonathan L Rees, Richard Craig, Navraj Nagra, Mathew Baldwin, Jennifer C E Lane, Andrew Price, David J Beard, Simon Abram, Andrew Judge, Daniel Prieto-Alhambra, Dominic Furniss, Andrew J Carr
Journal: BMJ (2022)

Abstract Objective To provide clinicians and patients with accurate risk estimates of serious adverse events after common elective shoulder arthroscopic procedures, including reoperation within one year. Design Population based cohort study. Setting Hospital Episode Statistics for NHS England, including civil registration mortality data from the Office for National Statistics. Participants 288 250 arthroscopic shoulder procedures performed in 261 248 patients aged ≥16 years between 1 April 2009 and 31 March 2017. Elective procedures were grouped into subacromial decompression, rotator cuff repair, acromioclavicular joint excision, glenohumeral stabilisation, and frozen shoulder release. Main outcome measures The primary outcomes were rates of serious adverse events (mortality, pulmonary embolism, pneumonia, myocardial infarction, acute kidney injury, stroke, and urinary tract infection) requiring inpatient care within 90 days post-surgery. Secondary outcomes were specific adverse event rates at 90 days, and reoperations (including for deep infection) within one year. Results The overall rate of complications within 90 days after arthroscopic shoulder surgery (including reoperation) was low at 1.2% (95% confidence interval 1.2% to 1.3%), with one in 81 patients at risk, and varied according to type of procedure, from 0.6% (0.5% to 0.8%) for glenohumeral stabilisation to 1.7% (1.5% to 1.8%) for frozen shoulder release. After adjustment for age, comorbidities, and sex, no effect of procedure type was observed. Pneumonia was the most common adverse event (0.3%, 0.3% to 0.4%), with one in 303 patients at risk. Pulmonary embolic events were rare, at 0.1% (0.1% to 0.1%), with one in 1428 patients at risk. At one year, the overall rate for reoperation was 3.8% (3.8% to 3.9%), with one in 26 patients at risk, ranging from 2.7% (2.5% to 3.0%) for glenohumeral stabilisation to 5.7% (5.4% to 6.1%) for frozen shoulder release. The overall rate of further surgery for deep infection was low, at 0.1% (0.1% to 0.1%), with one in 1111 patients at risk, but was higher after rotator cuff repair (0.2%, 0.2% to 0.2%), with one in 526 patients at risk. Over the study period the number of arthroscopic shoulder procedures increased, except for subacromial decompression, which decreased. Conclusions The findings of this study suggest that risks of serious adverse events associated with common shoulder arthroscopy procedures are low. Nevertheless, serious complications do occur, and include the risk of reoperation in one in 26 patients within one year. Study registration Clinical.Trials.gov NCT03573765 .
Translation of cytoplasmic UBA1 contributes to VEXAS syndrome pathogenesis
Authors: Marcela A. Ferrada, Sinisa Savic, Daniela Ospina Cardona, Jason C. Collins, Hugh Alessi, Fernanda Gutierrez-Rodrigues, Dinesh Babu Uthaya Kumar, Lorena Wilson, Wendy Goodspeed, James S. Topilow, Julie J. Paik, James A. Poulter, Tanaz A. Kermani, Matthew J. Koster, Kenneth J. Warrington, Catherine Cargo, Rachel S. Tattersall, Christopher J. A. Duncan, Anna Cantor, Patrycja Hoffmann, Elspeth M. Payne, Hanna Bonnekoh, Karoline Krause, Edward W. Cowen, Katherine R. Calvo, Bhavisha A. Patel, Amanda K. Ombrello, Daniel L. Kastner, Neal S. Young, Achim Werner, Peter C. Grayson, David B. Beck
Journal: Blood (2022)
Can group representations based on relational cues warrant the rich inferences typically drawn from group membership?
Authors: Katalin Oláh, Ildikó Király
Journal: Behavioral and Brain Sciences (2022)

Abstract Pietraszewski's model – though promising in many respects – needs to be extended so that it can explain the multitude of rich inferences that people draw from group membership. In this commentary, we highlight some facets of group thinking, especially from the field of developmental psychology, that cannot be unambiguously accounted for by a model that is built solely on relational cues.
scSTEM: clustering pseudotime ordered single-cell data
Authors: Qi Song, Jingtao Wang, Ziv Bar-Joseph
Journal: Genome biology (2022)

Abstract We develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metrics to summarize the expression of genes and assigns a p -value to clusters enabling the identification of significant profiles and comparison of profiles across different paths. Application of scSTEM to several scRNA-seq datasets demonstrates its usefulness and ability to improve downstream analysis of biological processes. scSTEM is available at https://github.com/alexQiSong/scSTEM .
DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk
Authors: Cynthia A. Kalita, Alexander Gusev
Journal: Genome biology (2022)

Abstract Here, we propose DeCAF (DEconvoluted cell type Allele specific Function), a new method to identify cell-fraction (cf) QTLs in tumors by leveraging both allelic and total expression information. Applying DeCAF to RNA-seq data from TCGA, we identify 3664 genes with cfQTLs (at 10% FDR) in 14 cell types, a 5.63× increase in discovery over conventional interaction-eQTL mapping. cfQTLs replicated in external cell-type-specific eQTL data are more enriched for cancer risk than conventional eQTLs. Our new method, DeCAF, empowers the discovery of biologically meaningful cfQTLs from bulk RNA-seq data in moderately sized studies.
Quantitative tissue analysis and role of myeloid cells in non-small cell lung cancer
Authors: Brian S Henick, Franz Villarroel-Espindola, Ila Datar, Miguel F Sanmamed, Jovian Yu, Shruti Desai, Alice Li, Adam Aguirre-Ducler, Konstantinos Syrigos, David L Rimm, Lieping Chen, Roy S Herbst, Kurt A Schalper
Journal: Journal for ImmunoTherapy of Cancer (2022)

Despite the prominent role of innate immunity in the antitumor response, little is known about the myeloid composition of human non-small cell lung cancer (NSCLC) with respect to histology and molecular subtype. We used multiplexed quantitative immunofluorescence (QIF) to measure the distribution and clinical significance of major myeloid cell subsets in large retrospective NSCLC collections. We established a QIF panel to map major myeloid cell subsets in fixed human NSCLC including 4',6-Diamidino-2-Phenylindole for all cells, pancytokeratin for tumor-epithelial cells, CD68 for M1-like macrophages; and CD11b plus HLA-DR to interrogate mature and immature myeloid cell populations such as myeloid derived suppressor cells (MDSCs). We interrogated 793 NSCLCs represented in four tissue microarray-based cohorts: #1 (Yale, n=379) and #2 (Greece, n=230) with diverse NSCLC subtypes; #3 (Yale, n=138) with molecularly annotated lung adenocarcinomas (ADC); and #4 (Yale, n=46) with patient-matched NSCLC and morphologically-normal lung tissue. We examined associations between marker levels, myeloid cell profiles, clinicopathologic/molecular variables and survival. The levels of CD68+ M1 like macrophages were significantly lower and the fraction of CD11b+/HLA-DR- MDSC-like cells was prominently higher in tumor than in matched non-tumor lung tissues. HLA-DR was consistently higher in myeloid cells from tumors with elevated CD68 expression. Stromal CD11b was significantly higher in squamous cell carcinomas (SCC) than in ADC across the cohorts and EGFR-mutated lung ADCs displayed lower CD11b levels than KRAS-mutant tumors. Increased stromal CD68- and HLA-DR-expressing cells was associated with better survival in ADCs from two independent NSCLC cohorts. In SCC, increased stromal CD11b or HLA-DR expression was associated with a trend towards shorter 5-year survival. NSCLCs display an unfavorable myeloid immune contexture relative to non-tumor lung and exhibit distinct myeloid-cell profiles across histologies and presence of major oncogenic driver-mutations. Elevated M1-like stromal proinflammatory myeloid cells are prognostic in lung ADC, but not in SCC.
Developmental antecedents of representing “group” behavior: A commentary on Pietraszewski's theory of groups
Authors: Anthea Pun, Andrew Baron
Journal: Behavioral and Brain Sciences (2022)

Abstract Central to Pietraszewski's theory is a set of group-constitutive roles within four triadic primitives. Although some data from the developmental and biological sciences support Pietraszewski's theory, other data raise questions about whether similar behavioral expectations hold across various ecological conditions and interactions. We discuss the potential for a broader set of conceptual primitives that support reasoning about groups.
Social groups and the computational conundrums of delays, proximity, and loyalty
Authors: Dragos Simandan
Journal: Behavioral and Brain Sciences (2022)

Abstract Even though Pietraszewski acknowledges the tentative nature of the theory and the multiple lines of adjacent research needed to flesh it out, he insists that the finite set of primitives he identified is necessary and sufficient for defining social groups in the context of conflict. In this commentary I expose three interrelated conundrums that cast doubt on this simplistic presumption.
Pathological complete response to immune checkpoint inhibitor in patients with colorectal cancer liver metastases harboring<i>POLE</i>exonuclease domain mutation
Authors: Lei Wen, Zhigang Chen, Xiaomeng Ji, William Pat Fong, Qiong Shao, Chao Ren, Yanyu Cai, Binkui Li, Yunfei Yuan, Deshen Wang, Yuhong Li
Journal: Journal for ImmunoTherapy of Cancer (2022)

Patients with polymerase epsilon ( POLE ) exonuclease domain mutation (EDM) exhibits distinct clinical characteristics and extremely high tumor mutation burden (TMB). There is a paucity of data on the therapeutic efficacy of immune checkpoint inhibitors (ICIs) for the treatment of colorectal cancer liver metastases (CRLM) patients with POLE EDM. Clinical characteristics, radiological and pathological response, as well as oncological outcomes of four CRLM patients harboring POLE EDM and treated by ICI plus chemotherapy were retrospectively collected and analyzed. TMB and genomic mutation profiling were also assessed in resected CRLM patients harboring different molecular characteristics. The four CRLM patients received toripalimab or sintilimab plus chemotherapy (FOLFOX or FOLFIRI or XELOX) with or without bevacizumab after POLE EDM were detected. All four patients achieved a radiological partial response. Staged or simultaneous complete surgical resection of the primary tumor and liver metastases was conducted. Pathological complete response was achieved in all four patients. After a median follow-up of 14 (range 9–20) months, all four patients maintained non-evidence of disease status until the last follow-up. POLE EDM patients showed a larger set of mutational genes compared with non- POLE EDM patients. TMB of patients harboring POLE EDM was significantly higher than those with microsatellite instability-high (median, 313.92 vs 42.24 mutations/Mb, p&lt;0.05), POLE non-EDM (313.92 vs 4.80, p&lt;0.001), and MSS subtypes (313.92 vs 4.80, p&lt;0.001). Despite being a rare phenotype, CRLM patients with POLE EDM exhibit ultra-high TMB and, more importantly, significant clinical response to ICI-based combination therapy. Therefore, the complete sequencing of POLE exonuclease domains is recommended in CRLM patients clinically.
Innovative strategies to improve hematopoietic stem cell transplant outcomes in myelofibrosis
Authors: Jacinta Perram, David M. Ross, Donal McLornan, Krisstina Gowin, Nicolas Kröger, Vikas Gupta, Clinton Lewis, Nico Gagelmann, Nada Hamad
Journal: American Journal of Hematology (2022)

Myelofibrosis (MF) is a clonal myeloproliferative neoplasm characterized by inflammation, marrow fibrosis, and an inherent risk of blastic transformation. Hematopoietic allogeneic stem cell transplant is the only potentially curative therapy for this disease, however, survival gains observed for other transplant indications over the past two decades have not been realized for MF. The role of transplantation may also evolve with the use of novel targeted agents. The chronic inflammatory state associated with MF necessitates pretransplantation assessment of end-organ function. Applying the transplant methodology employed for other myeloid disorders to patients with MF fails to acknowledge differences in the underlying disease pathophysiology. Limited understanding of the causes of poor transplant outcomes in this cohort has prevented refinement of transplant eligibility criteria in MF. There is increasing evidence of heterogeneity in molecular disease grade, beyond the clinical manifestations which have traditionally guided transplant timing. Exploring the physiological consequences of disease chronicity unique to MF, acknowledging the heterogeneity in disease grade, and using advanced prognostic models, molecular diagnostics and other organ function diagnostic tools, we present an innovative review of strategies with the potential to improve transplant outcomes in this disease. Larger, prospective studies which consider the impact of molecular-based disease grade are needed for MF transplantation.
Beyond folk-sociology: Extending Pietraszewski's model to large-group dynamics
Authors: Pascal Boyer
Journal: Behavioral and Brain Sciences (2022)

Folk-sociology is a set of intuitive assumptions that organize our spontaneous theories about society, including the notion that social groups are agent-like. Pietraszewski's model may explain this folk-sociological assumption in an elegant way. However, large-scale group dynamics include features that seem to escape agent-like descriptions. Therefore, one may want to find out whether the "event-grammar" proposed here can account for these features.